These data were published in Hu et al., 2016.
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This dataset is a raw output\u00a0operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from DNA and RNA. The numbers in each column represent the number of sequences from that sample belonging to a given OTU (row), with the last column listing the taxonomic ID assigned to each OTU.\u00a0The raw sequence data can be found in the NCBI SRA database under accession number\u00a0SRP070577\u00a0with the associated\u00a0BioProject\u00a0PRJNA311248.\u00a0 Metadata for these sequences can be found in the dataset:
\n\u201d18S rRNA gene tag sequences from DNA and RNA\": https://www.bco-dmo.org/dataset/745527
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Nucleotide bases with a Q score lower than 20 for the last 30 bp of each sequence were trimmed. Paired-end sequences were merged using FLASh (Magoc and Salzberg 2011) with a minimum of 10 bp and maximum of 150 bp overlap between each sequence pair. Sequences shorter than 350 bp, longer than 460 bp, or which had an average quality score lower than 25 were discarded using QIIME v1.8 (Caporaso et al. 2010). Chimeric sequences were identified and removed, by either de novo or reference-based chimera checking (identify chimeric seqs.py in QIIME, intersection method).\u00a0
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The code release v2 associated with this version of the dataset can be downloaded as a .zip file from the Supplemental\u00a0Documents section of this page. Future code updates will be accessible from the GitHub repository\u00a0https://github.com/shu251/V4_tagsequencing_18Sdiversity_q1.
This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from extracted DNA and RNA. Columns represent samples, including month sampled, material (either extracted RNA or DNA), and depth (in meters); thus values in each column represent the number of sequences in that sample that belong to a given OTU (OTUs by row). Each row represents a single OTU. The last column lists the taxonomic identifier assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248.
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Metadata for these sequences can be found in the dataset:
\n\u201d18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527
BCO-DMO Data Manager Processing Notes:
\n* data extracted from xlsx sheet to csv
\n* added a conventional header with dataset name, PI name, version date
\n* modified parameter names to conform with BCO-DMO naming conventions
\n* blank values in this dataset are displayed as "nd" for "no data." nd is the default missing data identifier in the BCO-DMO system.